Align GluB aka CGL1951, component of Glutamate porter (characterized)
to candidate WP_054653754.1 CES79_RS00810 transporter substrate-binding domain-containing protein
Query= TCDB::P48242 (295 letters) >NCBI__GCF_002217945.1:WP_054653754.1 Length = 277 Score = 109 bits (272), Expect = 8e-29 Identities = 85/276 (30%), Positives = 134/276 (48%), Gaps = 16/276 (5%) Query: 4 KRTFTRIGAILGATALAGVTLTACGDSSGGDGFLA--AIENGSVNVGTKYDQPGLGLRNP 61 K+ F + I+ + AL + LTACG D + A ++ ++ G K D GL + Sbjct: 2 KKLFRLVSVIVSSLALL-LVLTACGSKPLADQNVVTRAKQSNTITWGVKADTKLFGLMDV 60 Query: 62 DNS-MSGLDVDVAEYVVNSIADDKGWDHPTIEWRESPSAQRETLIQNGEVDMIAATYSIN 120 NS + G +VD+A+ + I KG ++ + S+ R L++NG +D I AT +I Sbjct: 61 KNSQIKGFEVDMAKALTKQILGPKG----KADFVQVTSSTRMPLLKNGNIDAIMATMTIT 116 Query: 121 AGRSESVNFGGPYLLTHQALLVRQDDDRIETLEDLD-NGLILCSVSGSTPAQKVKDVLPG 179 R + V+F Y Q+LLV+ + I+ ++DL+ NG + V GS Q V P Sbjct: 117 PERLKQVDFSRSYFDAGQSLLVK-NGSPIKNVKDLNKNGATVLGVVGSNSVQNVAKFAPK 175 Query: 180 VQLQEYDTYSSCVEALSQGNVDALTTDATILFGYSQQYEGDFRVVEMEKDGEPFTDEYYG 239 ++ + Y+ + AL G +ALTTD IL G S + G G FT E YG Sbjct: 176 AKVLQLSDYAQAMTALKSGQGEALTTDNGILAGMSVENPG------YHLAGGAFTKEPYG 229 Query: 240 IGLKKDDQEGTDAINAALERMYADGTFQRLLTENLG 275 I + K+ E +N AL ++ G + R+L + G Sbjct: 230 IAINKNQPEFKHDLNHALTKVEQSGQYNRILKKWFG 265 Lambda K H 0.312 0.133 0.378 Gapped Lambda K H 0.267 0.0410 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 1 Number of Hits to DB: 175 Number of extensions: 7 Number of successful extensions: 2 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 1 Number of HSP's successfully gapped: 1 Length of query: 295 Length of database: 277 Length adjustment: 26 Effective length of query: 269 Effective length of database: 251 Effective search space: 67519 Effective search space used: 67519 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.2 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 42 (21.8 bits) S2: 47 (22.7 bits)
This GapMind analysis is from Sep 24 2021. The underlying query database was built on Sep 17 2021.
Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.
A candidate for a step is "high confidence" if either:
Otherwise, a candidate is "medium confidence" if either:
Other blast hits with at least 50% coverage are "low confidence."
Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:
GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).
For more information, see:
If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know
by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory